Under The Cover
by ConstantlyCas
Summary: Was Khan really in control? Is he responsible for his actions? These are questions Kirk and Spock ask themselves when the new Admiral asks then to look into Khan's memories. All they know is that his crew is innocent, and they have to protect them from being taken, and becoming like their Captain. Warnings: torture will be involved in this story.
1. Chapter 1

**Hello! Beginnings of a story here, few chapters after this already written but thought if I posted this now I'd be more motivated to finish. This is just an idea I had and put a lot of thought into. Hope you enjoy it! Also I started writing this before Sherlock Series 3 come out (I know it was ages ago) so it kind of contradicts what happens then so just ignore its existence. Enjoy! **

Chapter 1

Kirk and Spock couldn't believe it. Starfleet had woken Khan up again! They didn't understand why they'd done it, hadn't they learnt from last time? Why was it that they thought they could control him? Both Spock and Kirk knew that Khan could be stopped, but controlled? It was near on impossible! At least not with any talent that they possessed. And why was it that they had been told to have a voice call with the new Admiral? Surely they didn't want them to take care of him? And why a voice call? Who does meetings like that anymore?

"Gentlemen," Admiral Jimmy Airort quipped, "Thank you for calling."

"You did not give us a lot of choice, _sir_," replied Spock, he'd been in a mood all morning, Kirk observed, but he didn't know why.

"Yes, well," Airort seemed to sense that the men before him had no interest in who he was, just who the person was who Admiral before him, "Anyway," Airort quickly moved on, "I suppose you've heard that Khan has been woken up?"

"How could we not?" Kirk laughed out in disbelief, _seriously who was this guy? _Kirk wondered.

"Well, I am getting the impression that you're becoming impatient, so I'll get right to it," Airort paused for a second, but it felt like a lifetime to Kirk. _This is it_, Kirk thought _He's going to make us watch over him and make him work and do all the stupid shit that Marcus did._

"I want you to look into his mind," Airort said calmly. Kirk and Spock blinked, once, twice. _Well, _thought Kirk, _that was unexpected. _

"Err, what?" Spock replied, _that's not like him_, Kirk observed, he was going to have to ask what was wrong with him later.

"I want to know why he did what he did," Airort specified, "and I thought the two of you would want to know too," _Okay, _Kirk thought, _still not really getting it._

"And, how exactly, would you like us to do that?" Kirk asked.

"I thought Spock here could do a mind-meld with him," Airort answered.

"I cannot. I have tried to read his past but could not see it." Spock argued, "He is too strong for me to force my way in, he would have to let me," not that Kirk thought Spock would do that unless it was in the heat of combat, he was too _proper _for that, even if he did hate the guy.

"Then ask him," Airort replied as if it was the simplest thing to do in the world.

"What do you mean, 'Then ask him', he'd never agree?!" Kirk responded in disbelief, _how did he even get this job?_ Kirk wondered.

"Look," Airort sighed, "I just want you to try, if you fail, you fail. But just try,"

"And what happens to Khan after?" Kirk quarried.

"That depends on what you find."

* * *

><p>"NO!" Khan shrieked, he did not take the idea well.<p>

"Come on Khan, what have you got to hide?" Kirk asked.

"Why do you want to know of my past anyway?!" Khan asked back.

"I want to understand why you did it!" shouted Spock. Kirk raised his eyebrows at that. Spock had just lost his temper, he never loses his temper.

"I am not letting you into my mind and that's that. You'll just have to force your way in," said Khan with anger and irritation on his face. _But really, has he had any other expression on his face since we've met him?_ Kirk thought.

"You know full well that I cannot force my way into your mind so far that I know everything," Spock argued.

"Didn't you get a good enough look last time you were in?" Khan spat back.

"That was by force and only showed how you were in that moment," Spock spat back to Khan. _Seriously, it was practically a spitting contest_ Kirk thought with frustration.

"You have no interest in why I did it. The only thing you care about is that I did do it," Khan spat (_seriously, what was it with the spitting_).

"No he doesn't care really," Kirk said calmly, "but I do,"

"Then why aren't you asking me, Captain?" Khan snarled (Kirk preferred the spitting).

"Because I'm not Vulcan, so I can't mind meld," he sighed, trying to look casual, "I'm only human,"

Khan stopped. But not in contemplation, in rage.

"You are making it sound like humans are worthless!" Khan raged.

"I believe that is what you think," Kirk said calmly back.

"I have never said that!" Khan was now becoming quite agitated.

"What happened to 'I am better'?" Kirk quarried with amusement in his voice, but not in his head.

"I am better!" Khan shouted, "But I am human in case that had escaped your attention," Well, it had actually.

"_Oh_," That was all Kirk could come up with to say. Khan looked almost...hurt by this. Kirk wouldn't have thought he wanted to be associated with humans, why would he be upset that he wasn't considered one.

"I'll show you if you promise me that my crew will be safe," Khan said with hesitation at great length. _There really wasn't anything he wouldn't do for his crew is there?_ thought Kirk.

"I will do my absolute best to ensure that your crew will be safe. But I am not above Starfleet, even though I act like it," Kirk said. He wasn't going to promise him anything that he couldn't do.

"Mr Spock?" Khan addressed Spock. Spock hesitated, but then said;

"Your crew has done nothing wrong as of yet, so I will not let them be hurt without just reason,"

Khan looked between them, and then sighed.

"It will have to do I suppose," sighed Khan. "But I want you to project this straight to Captain Kirk. I don't want you lying about what you will see,"

"Vulcans cannot lie." stated Spock.

"No, but humans can," Khan snapped. "One of our best qualities, don't you think?" _Ouch, that'll hit a nerve, _thought Kirk.

"I cannot project images I'm afraid," Spock said, trying to ignore Khan's last comment.

"Well lucky for you, I can," Khan replied with a smug look on his face. Kirk could punch that face. "I can project my memories into both your heads while Mr Spock does his mind meld to ensure that I am not lying," _Wow, this is very cooperative. He must really love his crew, _Kirk thought.

"Right then, let's get to it," Kirk said, and then the chaos began.

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**Comments are always appreciated! **


	2. Chapter 2

**Here's the next one guys. Forgot to clarify before that I don't own the characters or the shows, etc., you know the drill, disclaimer, no copy write intended, all that. Enjoy!**

Chapter 2

Sherlock Holmes wasn't having the best of lives. He had no friends, and his family hated him, well, except for Mycroft, but he was a fat pig so he doesn't count. Sherlock was too clever for his own good, people would say, but the truth was, Sherlock was too clever for the rest of the world. No one understood. No one saw the world the way he did. And it made him feel lonely. Everyone at school called him a freak, even the ones that were younger than him, and the older ones liked to use him as their human punching bag. He was alone. But he didn't really mind all that much. The others weren't like him, so why hang around with them? No. Sherlock much preferred to be alone with a good book.

Even through all the hell that school put him through, it was better than home. His father hated him. Sherlock wasn't sure what it exactly was that he was doing wrong, but his father was angry at him never the less. He would beat Sherlock, starve him, lock him in a cellar for days on end. His mother just sat idly by whilst it happened, and Mycroft was too afraid to stop him. But he did clean up Sherlock's wounds and snuck him food when his father gave him none. Mycroft was good to him, but Sherlock couldn't help but be angry at him for not stopping their father, especially when Mycroft left. Sherlock knew that he could never forgive Mycroft for leaving him there, alone.

Sherlock stormed his way through school, and University. But when the 21st century arrived, he was a mess. Mycroft had cut off his fund until Sherlock kicked the drugs, but he wouldn't. His landlord kicked him out and Sherlock took to the streets, doing anything he could to secure his next hit. It stayed this way for years. Mycroft came to Sherlock's aid when he needed it, but generally left him alone. He knew Sherlock hated him, it was no secret, and what he was doing now wouldn't help. But Mycroft refused to fund Sherlock's addictions, so he left him to make his own way, till he either kicked the drugs or asked him to take him to rehab.

One the 20th November 2005, Sherlock stumbled across a triple homicide crime scene before it had been properly closed off, and solved the case in about 18 seconds.

"It was the brother," was all he said. The police officers present whirled around to look at who had spoken and all turned their noses up at the homeless drug addict in disgust. Except one.

"What makes you say that?" the exception asked, Sherlock deduced that he was in charge here, probably a Detective Inspector.

"Because it was the brother," Sherlock replied as if the man were a child.

"Look mister," a curtain mouse-faced forensic officer began, "why don't you pop off to whatever dumpster it is you call home and let the real police do their work?" all the other officers snickered at that. Sherlock was use to it, so he paid no mind to it. He was turning away when the man in charge addressed him again.

"No, wait," he called, "how did you know?" Sherlock then began his very clever speech about what he had observed and the deductions he made to get to the conclusion that it was, in fact, the brother.

The officers stared at him in shock, till the leader spoke again.

"What's your name?" he asked.

"Sherlock Holmes," Sherlock replied.

"Well Mr Holmes..." the leader began.

"Please don't call me that," Sherlock cut in. He hated when people called him 'Mr Holmes', it reminded him too much of his father. No one ever called Mr Holmes 'Arthur', even his family referred to him as 'Sir', that was just how it was. So Sherlock avoided being called 'Mr Holmes' whenever he could.

"_Okay...Sherlock..._well what I was trying to say was that was bloody_ genius_! How did you do that?" Sherlock stared on in shock; no one had called him a genius before.

"Erm..." Sherlock tried.

"It's okay," the leader interrupted, "you don't have to answer that. Probably a thought process I could never understand," the leader licked his lips, "I'm Detective Inspector Gregory Lestrade, by the way," Lestrade held out his hand, and Sherlock shook it lightly.

And that was the start of Sherlock's career as a Consulting Detective.

Lestrade was there a lot for Sherlock, something he never really thanked him for. Lestrade took Sherlock in, cleaned him up, and kept him entertained with cases so he wouldn't get bored. When Mycroft found out about this, he instantly kidnapped Lestrade and interrogated him. But instead of Mycroft scaring Lestrade, Lestrade scared him.

And that was the start of a beautiful friendship.

5 years after Sherlock first met Lestrade, on the 25th July 2010, Sherlock stumbled across a man named John Watson. Now John was very different to everyone else, he was plain, ordinary, but by no means boring. Sherlock didn't know what it was. It could be because John called him brilliant, no one had done that before, or it could be because John took all the shit that Sherlock threw his way, but he stayed. John always stayed. Even when Sherlock jumped off a roof and came storming back into John's life three years later, John just fell right back in his place, by Sherlock's side, without question. Well, he got married so obviously there were some changes, but everything was still basically the same.

Sherlock discovered a long time ago that he loved John; it was obvious, to everyone, except John. Everyone also knew that John loved Sherlock on some level, but he hadn't realised it. 6 years they'd known each other, but John didn't know, so Sherlock gave up hope on that dream. He didn't mind though really, they were still basically a married couple, especially when John divorced Mary and moved back in with Sherlock, 2 years later, but still did not know his love for Sherlock.

It was the 8th year of their friendship that it happened, on the 26th April 2018. When life would never be the same. For anyone. But most of all, it was the day that Sherlock Holmes died.

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**Review please!**


	3. Chapter 3

Chapter 3

Sherlock and John where consulting on a case with Lestrade about a series of kidnappings. 15 people had been taken and there appeared to be no link between them except that they all happened in London. Some were elderly, some were children, adults, black, white, rich, poor, some didn't even live in London they were just on holiday's. A whole family was taken all in one swoop. Whatever the reason that they were being taken for, it was nothing good.

Sherlock was become quickly frustrated with the lack of leads and John was becoming very worried about him.

"Sherlock, you need to eat something," John said for the up most time during the past three days, "Just have a ham sandwich or something,"

"I have told you John," Sherlock growled, "Digestion slows me down,"

"Good," John replied, "You need a rest,"

"I'll rest when those people are safe and sound," little did Sherlock know at the time, that that achievement would take millennia.

"Sherlock..." John began.

"No!" Sherlock quickly cut off, with more force than intended. John didn't bring it up again.

Two days later, on the 26th April 2018, Sherlock stormed into Lestrade's office in New Scotland Yard, with a single pace of paper, held in his clenched, gloved hand.

"I've got a lead!" Sherlock had shouted, "One of my homeless network has seen men dragging people into a warehouse in far East London, and she thinks it's the people that have been taken," Sherlock was nearly jumping with excitement. He couldn't believe that he'd solved it, he had no doubt that the people would be in that warehouse. He should of.

"You think there still there," Lestrade questioned, grabbing his coat and signalling to Anderson and Donavon to do the same.

"She hasn't seen anyone but the men leave," Sherlock reported, striding towards the door with John at his heels, Lestrade, Anderson and Donavon trailing behind.

They were all so desperate to get to those people that they didn't bother getting a warrant or a team together, not that it mattered. No one would come out of that warehouse again.

* * *

><p>The five of them entered the warehouse very quietly, but they didn't see anyone, or hear anyone. They walked farther into the building, till they came to a strange light in the centre of the room. It was a huge circle filled with light that was on a platform that was only a few inches of the floor, they all stepped up onto this light to get a better look and what it was, something that they would regret for the rest of their lives,. For 10 seconds later, 10 long seconds, they weren't in that warehouse anymore, and they would never see it again.<p>

They were standing on another light circle, but as they looked around them, they were no longer in the same room. They began to panic, checked their heads for injury. They appeared to be somewhere that looked like a throne room. But all the fear of what had just happened disappeared into a far off part of their minds, and was replaced by absolute terror.

They looked up and saw the man who would ruin their lives, who had ruined them before.

They looked up and saw their new master, a master who they would never truly break free of.

They looked up, and saw the one man they thought they'd never see again.

They looked up and saw him.

Moriarty.

"Arh," Moriarty sighed in that high pitch squeak of a voice that is signature to the madman that stood before them, "New pets! And very interesting ones at that!" Moriarty jumped up from his throne and strode towards the group, frozen by terror. Even the Great Sherlock Holmes, who had so often been conserved as fearless, could not even blink in the presents of this monster of a man. He was the thing that Sherlock has nightmares about, it used to be his father, coming into his room for his next 'anger management session'. But nowadays it was the thing that now stood mere inches away from him, more importantly, that stood mere inches from his friends.

"Well," Moriarty began, bringing his eyes to look Sherlock directly in his, "not pets, more like lab rats," Sherlock was court like a deer in the headlight of Moriarty's gaze. He couldn't move. This man who he had believed to be dead, who he had watched, or at least thought he watched, put a bullet in his mouth, was once again before him. Ready to destroy his life in every way imaginable. Sherlock didn't know what he meant by 'lab rats', and he didn't care to find out, but he knew he had to save them all in that moment, or, what he later changed it to, as many as he could.

And it was this promise, this vow, that ended his life.

"What's the matter guys," Moriarty chirped, "Cat got your tongue?" Moriarty through his head back and laughed at the not at all funny joke. He stopped when he didn't get a raise out of his new lab rats. Sherlock moved passed his stunned stage and concentrated his gaze on Moriarty that showed his disgust in the man.

"How are you even alive?" Sherlock growled, "I saw you! You shot yourself straight in the mouth! I saw it! I watched it happen!" Sherlock couldn't believe it. He was dead! He stood mere inches away from it when it happened. There was no way he could have missed the fact that he survived. No. Way.

"Oh please Sherlock," Moriarty replayed, slightly disappointed, "You think you the only one who can fake their own death?"

"I didn't use a gun, and I didn't do it spontaneously," Sherlock snapped back. He saw John flinch at the statement in the corner of his eye. It was still a sore subject for John. Not the fact that he jumped of a roof, although that was pretty traumatic, but the fact that he knew it was going to happen but didn't come to him about it. After everything they'd been through, he still didn't ask for his help. He knew when Sherlock came back that it was because he needed to believe that Sherlock was dead to keep the both of them safe, but that didn't stop the heartache.

Moriarty noticed the glance the two sent each other and sighed.

"Oh were not on this again are we?" they gave him blank looks, "You know, the whole 'I love you but I've been straight my whole life', and the 'I'm not good at relationships' and all that crap." Moriarty looked almost pissed off at this, which Lestrade could relate with; it'd been going on for years.

"Well, you're clearly not in a chatty mood so let's get just hop right too it," he paused "Welcome to The Island." He looked at the group, "I know, I know. Not an impressive name, but hey, it is an island. My own privet island that no one knows about. Cliché? I know that too. But it just happens to be true. Isn't that amazing?" He let out a short laugh, and then stopped when he saw the others faces.

"Oh don't look so gloomy. You're all gonna take part in some very exciting things,"

"We will not take part in any more of your games Moriarty!" John yelled at him. He was done with his games, done with them a long time ago, and he wouldn't let Sherlock get strung in to them, he wasn't losing him again. John stepped forward and Sherlock put his arm in front of John to stop him from doing anything stupid. John looked into Sherlock's eyes and saw something there that was just screaming 'please, don't make me lose you', and John understood, he talk a step back.

"Aw, the obedient little soldier following his leader's every command," Moriarty patronised, "I don't know why I didn't think of involving you lot before!"

"Involving us in what Moriarty?" Lestrade asked, he was bored of questions with no answers.

My plan to rule the world my dear Inspector," Moriarty replayed, "Come on rats, I'll show you my organisation."

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	4. Chapter 4

**Short one, sorry. Also sorry for slow updating, I'll try to be faster is future, but can't promise anything. Thanks to everyone who has reviewed and followed/favourite the story, love you guys! Anyway I hope you enjoy this chapter!**

Chapter 4

It was horrifying. The land outside of the building they landed in stank. It smelt of blood and flesh and sweat and sick and shit and piss and all things terrible. Anderson was on the verge off empting his stomach onto the ground, adding to the stench.

People were huddled together and averted their eyes as Moriarty and his men walked by. There were all sought of people here. Children, adults, elderly, British, Russian, Chinese. There was a never ending variety of people, of all shapes and sizes. They were starving and cold and sick and injured and all kinds of deformed. All of them harboured long, deep cuts across their foreheads and every single one of them had blonde hair, whether in was natural or dyed.

The buildings were in ruins. They looked as if they were made of cardboard that had got wet in the rain, slowly pealing away from their original structure under the weight of the water. Some people were huddled inside of them, but most had the sense to see that it was safer on the streets, the damp would be no bother to them there. There were a few stone buildings scattered around, Sherlock presumed that this was for the main areas of Moriarty's organisation, whatever that was.

The roads where just mud paths. The only thing that told people it was a road where the tyre tracks that were imprinted in the mud. Huge dips in places were the trucks that drove along it got stuck and splattered mud on anything nearby, whether that be a wall or a child.

Sherlock couldn't get over the shear amount of people that littered the place like garbage.

"How many people are here?" Lestrade demanded more than asked.

"About a thousand!" Moriarty declared with glee. He looked very pleased with himself. The others were outraged by this fact. A _thousand? _"You know Sherlock," Moriarty began, "I'm surprised you didn't go straight to the question of 'How did we get here?' first. Is it your sentiments getting it the way again. Sherlock stayed silent. "_Aright_. Well I'll tell you anyway," he paused, probably for dramatic effect if John's experience of him was anything to go by. "It was a teleport,"

This did entice Sherlock, "_What?_" He asked in disbelief.

"So he does talk!" Moriarty stated with amusement, which was reserved by a glare from Sherlock. "I said a teleport. I've been doing a lot of clever things since we last met and I've hired a lot more people since your tore down my criminal web." Moriarty didn't look displeased by this, he was actually impressed. "_You _Sherlock, are going to be a very interesting to experiment on."

A look of terror crossed all their faces. Donavan and Anderson cowered behind the rest, John grabbed hold of Sherlock in a protective manner and Lestrade just look disgusted. Sherlock looked nothing short of terrified.

"You see," Moriarty said, talking to the group but concentrating on Sherlock, "I've done a lot on technology, all the things I need to rule the world, all the things I need to take over the world," he spoke as if he was listing the equipment that he had got to prepare dinner, like taking over the world was the easiest thing to do. It made him seem like a madman, but also made him someone to be _very _afraid of. "But then I thought, hang on, I need some body-guards, and then I thought hold on, I need some soldiers, and that is how I decided to experiment on people." He said it with such ease, such coolness, that it sent a shiver down the spines of everyone who heard his voice, and ice settle in the pits of their stomachs' which would never completely melt.

"You see, the way to be above everybody else, is to be more advanced than everybody else. It's not enough to have the technology if their man power is far superior to mine. I'll never have their numbers, so my men have to be more advanced, like my technology. I have scientists experimenting on ways to advance human nature, and there succeeding. Every person here are partaking in these experiments, even the children."

The reactions from before changed. Donavon and Anderson stood up straight from their cowering and looked around the people that surrounded them with looks of horror on their faces, holding each other tight. John's protective stance was still there, but half of his attention was also on the people around them, checking for any signs that what Moriarty was saying was true, and he found that there were. Lestrade's expression changed from disgust to down right anger as he looked at Moriarty, and took a protective stance in front of the others, subconsciously placing himself directly in front of Sherlock.

Sherlock however, was completely different. The movements Sherlock made where so quick, that they weren't even noticed. He pushed himself in front of Lestrade and dropped to his knees He didn't fall apart. He didn't beg. He just looked Moriarty in the eye with a stone-cold expression that had scared the living daylights out of so many people, and he just said….

"No."

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